Patent SG-11201903175V-A (SG)
Title: Efficient data structures for bioinformatics information representation
Inventor: RENZI DANIELE
IPC: G16B50/50
Filed: 2016-10-11
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property :::` , MD HIM 0 ill HON HI 1 0 0111011011H 101 010 EH 1111 OEN Organization International Bureau (10) International Publication Number 03 (43) International Publication Date .....•\"\"- WO 2018/068827 Al 19 April 2018 (19.04.2018) WIP0 1 PCT (51) International Patent Classification: MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, GOOF 19/28 (2011.01) GOOF 19/22 (2011.01) PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, (21) International Application Number: SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, PCT/EP2016/074297 TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (22) International Filing Date: (84) Designated States (unless otherwise indicated, for every 11 October 2016 (11.10.2016) kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (25) Filing Language: English UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (26) Publication Language: English TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, (71) Applicant: GENOMSYS SA [CH/CH]; Chemin de la Raye MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, 13, 1024 Ecublens VD (CH). TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). (72) Inventors: RENZI, Daniele; Route Aloys-Fauquez 105, 1018 Lausanne (CH). ZOIA, Giorgio; Chemin des Croix- Published: Rouges 10, 1007 Lausanne (CH). — with international search report (Art. 21(3)) (74) Agent: DE ANNA, Pier Luigi; Schubertstr. 10, 80336 Miinchen (DE). (81) Designated States (unless otherwise indicated, for every _ kind of national protection available): AE, AG, AL, AM, — AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, = CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, = DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, — HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KW, — KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, = = (54) Title: EFFICIENT DATA STRUCTURES FOR BIOINFORMATICS INFORMATION REPRESENTATION = 131 133 = 135 Raw 132 Aligned 134 genomic _,/ 136 = sequence Reads 7 --- - = Genome data data ---* Reads classes —.... Layers — = Sequencing Aligner classificator encoder 137 ---- \ 130 1311 139 = 1316 1312 1310 (-='.. = --) MIT and AUs with Syntax elements layers 138 = essed Compr Entropy Nis 4 _ MIT header _ Header and = Storage ' data Compressor encoder AU encoder J = - 1315 Updated data Analysis/ 1319 Genome Decompression Update Sequencing \s--- li Decomp 1314 1313 ressed data 1318 IN ei cc 1317 GC Figure 13 - Overall Architecture. , tD 0 —.... pc (57) : Method and apparatus for the representation of genome sequence data organized in a structured file format. The data 1-1 structure contains the representation of nucleotide sequences: in compressed form, aligned and referenced to one or more reference 0 el sequences and classified according to different degrees of matching accuracy. The classified and aligned reads are coded in the form 0 ., of layers of syntax elements, which including a header information are partitioned into independent or dependent access units. ..)